摘要
为了分析栽培莴苣Lactuca sativa‘Salinas’和野生莴苣Lactuca saligna的线粒体基因组密码子使用特征差异,对2种莴苣的线粒体基因组编码序列进行密码子使用偏好性研究,比较其密码子偏好性形成的影响因素和演化过程。结果表明:栽培莴苣和野生莴苣线粒体编码基因的总GC含量分别为43.43%和42.54%,富含A/T碱基。2种莴苣的有效密码子数(ENC)都在36.61~61.00,密码子偏好性较弱。中性绘图分析表明,2种莴苣线粒体编码基因的第1、2位和第3位碱基GC含量较为保守,选择是影响2种莴苣线粒体基因密码子使用偏好性的主要因素。PR2-plot分析表明,2种莴苣线粒体基因第3位碱基更偏好使用嘧啶碱基。ENC-plot分析结果显示,2种莴苣的线粒体基因密码子偏好性主要受到选择压力影响。对2种莴苣的相对同义密码子使用度(RSCU)分析表明,栽培莴苣和野生莴苣分别有28个和29个高频密码子,除亮氨酸外,2种莴苣的高频密码子均以A/U结尾。2种莴苣线粒体编码基因的密码子使用偏好性总体上较接近,但最优密码子存在较大差异。这种差异可能是因为2种莴苣的低表达基因库差异造成的,也可能与选择压力及人工育种对栽培莴苣线粒体基因组进化的影响有关。
In order to analyze codon usage bias of mitochondrial(mt)genomes of cultivated and wild lettuces(Lactuca sativa‘Salinas’and Lactuca saligna),this study investigated and compared the impact factors and evolutionary process of codon usage bias of the two lettuce mt coding sequences(CDS).The results showed that the overall GC contents of L.sativa‘Salinas’and L.saligna mt CDS were 43.43%and 42.54%,respectively.The mt genomes of both species had abundant A/T nucleotide bases.The effective number of codons(ENCs)of both species were from 36.61 to 61.00,indicating that the codon usage bias of the two species were not very strong.The analysis of neutrality plot found that the GC contents of the first,second,and the third bases were conserved.Selective pressure was the main impact factor of the codon usage bias of the two lettuce species.The PR2-plot analysis showed that the third nucleotide bases of the codons of the two lettuce mt genomes preferred to use pyrimidines.The results of ENC-plot analysis indicated that the codon usage of cultivated and wild lettuces was mostly affected by selection.The relative synonymous codon usage(RSCU)analysis indicated that L.sativa‘Salinas’and L.saligna had 28 and 29 codons with RSCU higher than 1.All of the codons ended with A and U bases,except for Leu.This study finds the codon usage of L.sativa‘Salinas’and L.saligna mt CDS similar in general,but different in optimal codons.These differences may come from different low expression gene libraries of the two species,or be caused by the effect of selection pressure and human selection of cultivated lettuce breeding on mt genome evolution.
作者
张扬
孙曙光
李晴
魏珍
ZHANG Yang;SUN Shuguang;LI Qing;WEI Zhen(Henan Academy of Agricultural Sciences,Zhengzhou 450002,China;Henan Institute of Crops Molecular Breeding,Zhengzhou 450002,China;School of Life Sciences,Zhengzhou University,Zhengzhou 450001,China)
出处
《河南农业科学》
北大核心
2022年第10期114-124,共11页
Journal of Henan Agricultural Sciences
基金
国家自然科学基金项目(31700175)
河南省重点研发专项(221111110800)
郑州大学青年教师基础研究培育基金项目(JC21343014)。
